Mercurial > repos > fubar > tool_factory_2

comparison toolfactory/install_tf_demos.py @ 119:8ea1133b9d9a draft

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author fubar
date Tue, 05 Jan 2021 00:34:48 +0000
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118:e43c43396a70 119:8ea1133b9d9a
1 import argparse
2 import os
3 import subprocess
4 import sys
5 import urllib.request
6
7 from bioblend import galaxy
8
9 WF = "https://drive.google.com/uc?export=download&id=13xE8o7tucHGNA0qYkEP98FfUGl2wdOU5"
10 HIST = (
11 "https://drive.google.com/uc?export=download&id=1V0ZN9ZBuqcGJvt2AP7s3g0q11uYEhdDB"
12 )
13 WF_FILE = "tf_workflow.ga"
14 HIST_FILE = "tf_history.tgz"
15
16
17 def _parser():
18 parser = argparse.ArgumentParser()
19 parser.add_argument(
20 "-g", "--galaxy", help="URL of target galaxy", default="http://localhost:9090"
21 )
22 parser.add_argument("-a", "--key", help="Galaxy admin key", default=None)
23 return parser
24
25
26 def main():
27 """
28 load the planemo tool_factory demonstration history and tool generating workflow
29 fails in planemo served galaxies because there seems to be no user in trans?
30 """
31 args = _parser().parse_args()
32 urllib.request.urlretrieve(WF, WF_FILE)
33 urllib.request.urlretrieve(HIST, HIST_FILE)
34 assert args.key, "Need an administrative key for the target Galaxy supplied please"
35 wfp = os.path.abspath(WF_FILE)
36 hp = os.path.abspath(HIST_FILE)
37 gi = galaxy.GalaxyInstance(
38 url=args.galaxy, key=args.key, email="planemo@galaxyproject.org"
39 )
40 x = gi.workflows.import_workflow_from_local_path(WF_FILE, publish=True)
41 print(f"installed {WF_FILE} Returned = {x}\n")
42 x = gi.histories.import_history(file_path=HIST_FILE)
43 print(f"installed {HIST_FILE} Returned = {x}\n")
44
45
46 if __name__ == "__main__":
47 main()